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rli012 / GDCRNATools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC
Apache License 2.0
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gdcParseMetadata error #15

Open Liripo opened 4 years ago

Liripo commented 4 years ago

gdcParseMetadata error

> metaMatrix.RNA <- gdcParseMetadata(metafile = "./metadata.cart.2020-05-08.json")
Error in vapply(seq_len(nSam), function(i) metadata[[i]]$cases[[1]]$samples[[1]]$submitter_id,  : 
  值的长度必需为1，
 但FUN(X[[1]])结果的长度却是0

The metadata.cart.2020-05-08.json file head is

[{
  "file_id": "ccf08842-c001-43be-b2c4-7a37499dcd18", 
  "associated_entities": [
    {
      "entity_submitter_id": "TCGA-71-6725-01A-11R-1858-07", 
      "entity_id": "9680a78d-59ab-4cf0-bd92-e6ecbc640e04", 
      "entity_type": "aliquot", 
      "case_id": "4b7cd595-e7f9-45a8-b736-a8c7c42d9539"
    }
  ], 
  "state": "released", 
  "submitter_id": "5d420937-4d97-4f04-9ce9-754054261d97_count", 
  "file_name": "5d420937-4d97-4f04-9ce9-754054261d97.htseq.counts.gz", 
  "experimental_strategy": "RNA-Seq", 
  "access": "open", 
  "data_format": "TXT", 
  "data_type": "Gene Expression Quantification", 
  "data_category": "Transcriptome Profiling", 
  "analysis": {
    "analysis_id": "390fff89-0e17-41c2-b0c5-2de8124271f0", 
    "input_files": [
      {
        "file_id": "745f6641-f01a-4c42-9883-f36872514020", 
        "state": "released", 
        "updated_datetime": "2018-11-15T21:12:37.513272-06:00", 
        "data_category": "Sequencing Reads", 
        "created_datetime": "2016-05-27T22:03:53.926564-05:00", 
        "file_name": "792a9dd3-28b5-42f5-aa23-e64f47995f9a_gdc_realn_rehead.bam", 
        "experimental_strategy": "RNA-Seq", 
        "access": "controlled", 
        "data_format": "BAM", 
        "data_type": "Aligned Reads", 
        "submitter_id": "792a9dd3-28b5-42f5-aa23-e64f47995f9a", 
        "md5sum": "d95c94ce0b5f02e70c6e7df27dc7d478", 
        "file_size": 10602206295, 
        "platform": "Illumina"
      }
    ], 
    "workflow_link": "https://github.com/NCI-GDC/htseq-cwl", 
    "updated_datetime": "2018-09-06T21:10:41.393019-05:00", 
    "submitter_id": "5d420937-4d97-4f04-9ce9-754054261d97_count", 
    "created_datetime": "2016-05-29T10:24:46.178710-05:00", 
    "state": "released", 
    "workflow_version": "v1", 
    "workflow_type": "HTSeq - Counts"
  }, 
  "md5sum": "f8b64783717da58198a723cfa52f0723", 
  "file_size": 254695
}
jiangzh-coder commented 4 years ago

i met the same problem, hopefully auther will answer !

Oxalin commented 2 years ago

I'm getting the same error. Did you find a workaround or a solution?